<div dir="ltr">Hi Felix,<div><br></div><div>From your stack trace, it looks like you are likely calling Bio-Formats from ImageJ.</div><div><br></div><div>In which case, you may want to read this article as well:</div><div><br></div><div> <a href="http://imagej.net/Logging">http://imagej.net/Logging</a></div><div><br></div><div>Contributions to that wiki page are welcome, e.g. if you have success configuring logging in novel ways.</div><div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Oct 22, 2015 at 10:37 AM, David Gault (Staff) <span dir="ltr"><<a href="mailto:d.gault@dundee.ac.uk" target="_blank">d.gault@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p><br>
</p>
<p><span></span>I Felix,</p>
<p><br>
</p>
<p>Just as a follow up to the information provided earlier, if you require a finer level of tuning for your logging then you can also make use of standard Logback configuration.</p>
<p><br>
</p>
<p>In order to do so you must first add the logback.xml file to your class path. </p>
<p>Note this will override the DebugTools.enableLogging(...) setting.</p>
<p><br>
</p>
<p>In this configuration you can define the level of logging specific to individual components. For example:</p>
<p><span lang="EN-GB"></span></p>
<blockquote style="margin-right:0px" dir="ltr">
<p style="margin-right:0px" dir="ltr"><font style="color:rgb(75,165,36)"><span style="color:rgb(75,165,36)"><logger</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">name</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"loci.formats.FormatHandler"</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">level</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"ERROR"</span><span style="color:rgb(75,165,36)">
</span>/></font></p>
<p style="margin-right:0px" dir="ltr"><font style="color:rgb(75,165,36)"><span style="color:rgb(75,165,36)"><logger</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">name</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"loci.formats.tiff.TiffParser"</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">level</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"DEBUG"</span><span style="color:rgb(75,165,36)">
</span>/></font></p>
</blockquote>
<p></p>
<p></p>
<p>Different appenders can also be configured to write output from specific loggers to various sources.
</p>
<p>In the example below all log messages will be sent to the console but only requests from FromatHandler and its children will be sent to the log file.</p>
<blockquote style="margin-right:0px" dir="ltr">
<p><span style="color:rgb(75,165,36)"><span style="color:rgb(75,165,36)"><configuration></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><appender</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">name</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"FILE"</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">class</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"ch.qos.logback.core.FileAppender"</span><span style="color:rgb(75,165,36)">></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><file>formatHandler</span><span style="color:rgb(75,165,36)">.log</span><span style="color:rgb(75,165,36)"></file></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><encoder></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><pattern></span><span style="color:rgb(75,165,36)">%date %level [%thread] %logger{10} [%file:%line] %msg%n</span><span style="color:rgb(75,165,36)"></pattern></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></encoder></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></appender></span><span style="color:rgb(75,165,36)"><br>
<br>
</span><span style="color:rgb(75,165,36)"><appender</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">name</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"STDOUT"</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">class</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"ch.qos.logback.core.ConsoleAppender"</span><span style="color:rgb(75,165,36)">></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><encoder></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><pattern></span><span style="color:rgb(75,165,36)">%msg%n</span><span style="color:rgb(75,165,36)"></pattern></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></encoder></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></appender></span><span style="color:rgb(75,165,36)"><br>
<br>
</span><span style="color:rgb(75,165,36)"><logger</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">name</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"loci.formats.FormatHandler"</span><span style="color:rgb(75,165,36)">></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><appender-ref</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">ref</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"FILE"</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">/></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></logger></span><span style="color:rgb(75,165,36)"><br>
<br>
</span><span style="color:rgb(75,165,36)"><root</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">level</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"debug"</span><span style="color:rgb(75,165,36)">></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"><appender-ref</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">ref</span><span style="color:rgb(75,165,36)">=</span><span style="color:rgb(75,165,36)">"STDOUT"</span><span style="color:rgb(75,165,36)">
</span><span style="color:rgb(75,165,36)">/></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></root></span><span style="color:rgb(75,165,36)"><br>
</span><span style="color:rgb(75,165,36)"></configuration></span></span></p>
</blockquote>
<p><span>Other useful things that can be defined in the LogBack configuration include registering status listeners, setting properties, variables and conditional processing.</span>For further configuration details and more complex examples you can
read more at the link below:</p>
<p><a href="http://logback.qos.ch/manual/configuration.html" target="_blank">http://logback.qos.ch/manual/configuration.html</a></p>
<p></p>
<div style="width:100%;overflow:auto;margin-top:20px;margin-bottom:20px;display:inline-block">
<table style="width:80%;overflow:auto;border-top-color:rgb(204,204,204);border-bottom-color:rgb(204,204,204);border-top-width:1px;border-bottom-width:1px;border-top-style:solid;border-bottom-style:solid;background-color:rgb(255,255,255)">
<tbody>
<tr valign="top" style="border-spacing:0px">
<td style="width:250px;padding-right:20px;vertical-align:middle;display:table-cell" colspan="1">
<div style="padding:0px;width:250px;min-height:73px;margin-top:12px;display:table;background-color:rgb(255,255,255)">
<a style="text-align:center;display:table-cell" href="http://logback.qos.ch/manual/configuration.html" target="_blank"><img width="250" height="73" style="border-width:0px;width:250px;min-height:73px;margin-right:auto;margin-left:auto;display:inline-block;max-height:250px;max-width:250px" src="http://logback.qos.ch/manual/images/chapters/configuration/lbClassicStatus.jpg"></a></div>
</td>
<td>
<div style="color:rgb(51,51,51);font-family:"wf_segoe-ui_semilight","Segoe UI Semilight","Segoe WP Semilight","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:21px;margin-top:8px;margin-right:14px;margin-left:14px">
Chapter 3: Configuration - Logback Home</div>
<div style="color:rgb(102,102,102);font-family:"wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:13px;margin-top:8px;margin-right:14px;margin-left:14px">
We start by presenting ways for configuring logback, with many example configuration scripts. Joran, the configuration framework upon which logback relies will ...</div>
<div style="margin:8px 14px 10px;min-height:18px;overflow:hidden;white-space:nowrap">
<a style="font-family:"wf_segoe-ui_normal","Segoe UI","Segoe WP",Tahoma,Arial,sans-serif;font-size:11px;text-decoration:none" href="http://logback.qos.ch/manual/configuration.html" target="_blank">Read
more...</a></div>
</td>
</tr>
</tbody>
</table>
</div>
<br>
<p>With Thanks,</p>
<p>David Gault</p>
<br>
<br>
<div style="color:rgb(0,0,0)">
<hr style="width:98%;display:inline-block">
<div dir="ltr"><font color="#000000" face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b> ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" target="_blank">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of David Gault (Staff) <<a href="mailto:d.gault@dundee.ac.uk" target="_blank">d.gault@dundee.ac.uk</a>><br>
<b>Sent:</b> 22 October 2015 13:49<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] SlideBookReader Error + DEBUG output</font>
<div> </div>
</div><div><div class="h5">
<div>Hi Felix,
<div><br>
</div>
<div>In order to configure the logging level I can recommend using the following utility class <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.4/api/loci/common/DebugTools.html#enableLogging(java.lang.String)" target="_blank">http://downloads.openmicroscopy.org/bio-formats/5.1.4/api/loci/common/DebugTools.html#enableLogging(java.lang.String)</a></div>
<div>So you can add the following to your code for example: </div>
<div><span style="font-family:Monaco;font-size:11px">DebugTools.enableLogging(</span><span style="color:rgb(57,51,255);font-family:Monaco;font-size:11px">"ERROR"</span><span style="font-family:Monaco;font-size:11px">);</span></div>
<div><br>
</div>
<div>The exception that you are seeing in the logs is indeed due to a library being unavailable. This particular reader still has further development required, including around the loading of libraries. The exception shown is caught and handled but is output
to the logger as a debug level log entry.</div>
<div><br>
</div>
<div>With Thanks,</div>
<div>David Gault</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 21 Oct 2015, at 16:15, MEYENHOFER Felix <<a href="mailto:felix.meyenhofer@unifr.ch" target="_blank">felix.meyenhofer@unifr.ch</a>> wrote:</div>
<br>
<div>Hi <br>
<br>
Whenever I call a bio-formats reader the error further down shows up. It continues to run, but I wonder if this is just an info, that we are missing the license? However as long as we don’t use the slidebookreader, I don’t see why it’s throwing an error instead
of a warning.<br>
<br>
Also I was wondering how to turn of the DEBUG output of Bio-Formats?<br>
<br>
<br>
17:04:00.645 [SciJava-35e0c0f9-Thread-2] DEBUG loci.formats.FormatHandler - 3i SlideBook SlideBook6Reader library not found. Please see
<a href="http://www.openmicroscopy.org/site/support/bio-formats/formats/3i-slidebook.html" target="_blank">
http://www.openmicroscopy.org/site/support/bio-formats/formats/3i-slidebook.html</a> for details.<br>
java.lang.UnsatisfiedLinkError: null<br>
<span style="white-space:pre-wrap"></span>at loci.formats.in.SlideBook6Reader.<clinit>(SlideBook6Reader.java:90) ~[formats-gpl-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at java.lang.Class.forName0(Native Method) [na:1.8.0_40]<br>
<span style="white-space:pre-wrap"></span>at java.lang.Class.forName(Class.java:264) [na:1.8.0_40]<br>
<span style="white-space:pre-wrap"></span>at loci.formats.ClassList.<init>(ClassList.java:127) [formats-api-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at loci.formats.ClassList.<init>(ClassList.java:85) [formats-api-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:78) [formats-api-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at loci.formats.ImageReader.<init>(ImageReader.java:115) [formats-api-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at loci.formats.ReaderWrapper.<init>(ReaderWrapper.java:62) [formats-api-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at loci.formats.ChannelSeparator.<init>(ChannelSeparator.java:78) [formats-bsd-5.1.5.jar:5.1.5]<br>
<span style="white-space:pre-wrap"></span>at NdpiTileColorSeparator.tile2GcStack(NdpiTileColorSeparator.java:219) [classes/:na]<br>
<span style="white-space:pre-wrap"></span>at NdpiTileColorSeparator.run(NdpiTileColorSeparator.java:123) [classes/:na]<br>
<span style="white-space:pre-wrap"></span>at org.scijava.command.CommandModule.run(CommandModule.java:201) [scijava-common-2.47.0.jar:2.47.0]<br>
<span style="white-space:pre-wrap"></span>at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) [scijava-common-2.47.0.jar:2.47.0]<br>
<span style="white-space:pre-wrap"></span>at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) [scijava-common-2.47.0.jar:2.47.0]<br>
<span style="white-space:pre-wrap"></span>at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) [scijava-common-2.47.0.jar:2.47.0]<br>
<span style="white-space:pre-wrap"></span>at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191) [scijava-common-2.47.0.jar:2.47.0]<br>
<span style="white-space:pre-wrap"></span>at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_40]<br>
<span style="white-space:pre-wrap"></span>at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_40]<br>
<span style="white-space:pre-wrap"></span>at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_40]<br>
<span style="white-space:pre-wrap"></span>at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]<br>
<br>
<br>
Best regards, <br>
<br>
-------------------------------------<br>
Felix Meyenhofer<br>
University of Fribourg<br>
Departement of Medicine - Anatomy<br>
1, Rte. Albert Gockel<br>
CH-1700 Fribourg <br>
<br>
Tel: <a href="tel:%2B41%2026%20300%2085%2045" value="+41263008545" target="_blank">+41 26 300 85 45</a><br>
Web: <a href="http://www.unifr.ch/anatomy" target="_blank">www.unifr.ch/anatomy</a><br>
<a href="http://www.unifr.ch/bioimage" target="_blank">www.unifr.ch/bioimage</a><br>
-------------------------------------<br>
<br>
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</blockquote>
</div>
<br>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
</div></div></div>
</div><div><div class="h5">
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div></div></div>
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